ubic.gemma.model.expression.experiment

Class ExperimentalFactor

java.lang.Object

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.expression.experiment.ExperimentalFactor

All Implemented Interfaces:

gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Serializable, Describable, Identifiable

public class ExperimentalFactor
extends AbstractDescribable
implements gemma.gsec.model.SecuredChild, Serializable

ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).

Author:

Paul

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ExperimentalFactor.Factory

Constructor Summary

Constructors

Constructor and Description
ExperimentalFactor() No-arg constructor added to satisfy javabean contract

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj) Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity.
Set<Characteristic>	getAnnotations()
Characteristic	getCategory() Obtain the category of this experimental factor.
ExperimentalDesign	getExperimentalDesign()
Set<FactorValue>	getFactorValues()
gemma.gsec.model.Securable	getSecurityOwner()
FactorType	getType()
int	hashCode() Returns a hash code based on this entity's identifiers.
void	setAnnotations(Set<Characteristic> annotations)
void	setCategory(Characteristic category)
void	setExperimentalDesign(ExperimentalDesign experimentalDesign)
void	setFactorValues(Set<FactorValue> factorValues)
void	setSecurityOwner(ExpressionExperiment securityOwner)
void	setType(FactorType type)

Methods inherited from class ubic.gemma.model.common.AbstractDescribable

getDescription, getId, getName, setDescription, setId, setName, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface gemma.gsec.model.Securable

getId

Constructor Detail

ExperimentalFactor

public ExperimentalFactor()

No-arg constructor added to satisfy javabean contract

Method Detail

hashCode

public int hashCode()

Description copied from class: AbstractDescribable

Returns a hash code based on this entity's identifiers.

Overrides:

hashCode in class AbstractDescribable

equals

public boolean equals(Object obj)

Description copied from class: AbstractDescribable

Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity. Returns false otherwise.

Overrides:

equals in class AbstractDescribable

getSecurityOwner

public gemma.gsec.model.Securable getSecurityOwner()

Specified by:

getSecurityOwner in interface gemma.gsec.model.SecuredChild

setSecurityOwner

public void setSecurityOwner(ExpressionExperiment securityOwner)

Parameters:

securityOwner - Used to hint the security system about who 'owns' this,

getAnnotations

public Set<Characteristic> getAnnotations()

setAnnotations

public void setAnnotations(Set<Characteristic> annotations)

getCategory

@Nullable
public Characteristic getCategory()

Obtain the category of this experimental factor.

Returns:

the category or null if annotated automatically from GEO or used as a dummy.

setCategory

public void setCategory(@Nullable
                        Characteristic category)

getExperimentalDesign

public ExperimentalDesign getExperimentalDesign()

setExperimentalDesign

public void setExperimentalDesign(ExperimentalDesign experimentalDesign)

getFactorValues

public Set<FactorValue> getFactorValues()

Returns:

The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.

setFactorValues

public void setFactorValues(Set<FactorValue> factorValues)

getType

public FactorType getType()

Returns:

Categorical vs. continuous. Continuous factors must have a 'measurement' associated with the factorvalues, Categorical ones must not.

setType

public void setType(FactorType type)